SCOTUS can't just "invalidate" an Executive Order like how they can invalidate an unconstitutional law (judicial review). The court system doesn't work like that. No one would have standing to bring such a case, nor does the judicial branch have authority over executive branch internal communications.

What could happen is that a federal agency follows an EO in a manner contrary to law, and that action causes some sort of harm or loss to a person. That injured party could then bring a legal action against the agency and the Court could order the agency to cease that action. But it still wouldn't invalidate the EO.

And the President’s order compels them to ignore that contradictory opinion.

You keep arguing the same point in this thread. So let’s make it simple.

If Congress or the SCOTUS says do A and the President says do B then the Executive Branch are required to do B.

That’s an unprecedented situation.